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SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

3,844

Mean Reads per Cell

71,840

Median Genes per Cell

1,093
Number of Reads
Total number of single-end reads that were sequenced.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist.
Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the transcriptome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped to the exonic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped to the intronic regions of the genome with a high mapping quality score as reported by the aligner.
Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped to the intergenic regions of the genome with a high mapping quality score as reported by the aligner.
Sequencing Saturation
The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene). This metric was called "cDNA PCR Duplication" in versions of Cell Ranger prior to 1.2.
Q30 Bases in Barcode
Fraction of bases with Q-score at least 30 in the cell barcode sequences.
Q30 Bases in RNA Read
Fraction of bases with Q-score at least 30 in the RNA read sequences. This is Illumina R1 for the Single Cell 3' v1 chemistry and Illumina R2 for the Single Cell 3' v2 chemistry.
Q30 Bases in Sample Index
Fraction of bases with Q-score at least 30 in the sample index sequences.
Q30 Bases in UMI
Fraction of bases with Q-score at least 30 in the UMI sequences.

Sequencing

Number of Reads 276,156,675
Valid Barcodes 98.3%
Reads Mapped Confidently to Transcriptome 56.2%
Reads Mapped Confidently to Exonic Regions 60.6%
Reads Mapped Confidently to Intronic Regions 27.2%
Reads Mapped Confidently to Intergenic Regions 4.1%
Sequencing Saturation 87.8%
Q30 Bases in Barcode 97.8%
Q30 Bases in RNA Read 73.5%
Q30 Bases in Sample Index 94.3%
Q30 Bases in UMI 97.9%
 
Estimated Number of Cells
The total number of barcodes associated with cell-containing partitions, estimated from the barcode count distribution.
Fraction Reads in Cells
The fraction of barcoded, confidently mapped reads with cell-associated barcodes.
Mean Reads per Cell
The total number of sequenced reads divided by the number of barcodes associated with cell-containing partitions.
Median Genes per Cell
The median number of genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
Total Genes Detected
The number of genes with at least one count in any cell.
Median UMI Counts per Cell
The median number of UMI counts per cell-associated barcode.

Cells

Estimated Number of Cells 3,844
Fraction Reads in Cells 88.0%
Mean Reads per Cell 71,840
Median Genes per Cell 1,093
Total Genes Detected 18,443
Median UMI Counts per Cell 3,640

Sample

Name pilot3_lane_2
Description
Transcriptome hg19
Chemistry Single Cell 3' v2
Cell Ranger Version 1.3.0

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